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- PDB-1k9g: Crystal Structure of the Complex of Cryptolepine-d(CCTAGG)2 -

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Basic information

Entry
Database: PDB / ID: 1k9g
TitleCrystal Structure of the Complex of Cryptolepine-d(CCTAGG)2
Components5'-D(*CP*CP*TP*AP*GP*G)-3'
KeywordsDNA / DNA intercalator complex
Function / homology5-METHYL-5H-INDOLO[3,2-B]QUINOLINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLisgarten, J.N. / Coll, M. / Portugal, J. / Wright, C.W. / Aymami, J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The antimalarial and cytotoxic drug cryptolepine intercalates into DNA at cytosine-cytosine sites.
Authors: Lisgarten, J.N. / Coll, M. / Portugal, J. / Wright, C.W. / Aymami, J.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*CP*TP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2743
Polymers1,8091
Non-polymers4652
Water66737
1
A: 5'-D(*CP*CP*TP*AP*GP*G)-3'
hetero molecules

A: 5'-D(*CP*CP*TP*AP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5486
Polymers3,6182
Non-polymers9294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)29.960, 29.960, 39.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe double helix is generated by the operation -x,-y+2,z.

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Components

#1: DNA chain 5'-D(*CP*CP*TP*AP*GP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DR1 / 5-METHYL-5H-INDOLO[3,2-B]QUINOLINE / CRYPTOLEPINE


Mass: 232.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Magnesium acetate, MES, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mMmagnesium acetate11
225 mMMES11pH6.5
31.25 Mammonium sulfate11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 3543 / Num. obs: 3356 / % possible obs: 87.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.1
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / Num. unique all: 292 / % possible all: 73.2
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 73.2 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.227 167 RANDOM
Rwork0.208 --
all0.209 3356 -
obs0.209 3356 -
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 36 37 193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.023
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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